4L0W

Plasmodium yoelii Prx1a modified at the N-terminus forms an artifactual octamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2h01


Literature

Observed octameric assembly of a Plasmodium yoelii peroxiredoxin can be explained by the replacement of native "ball-and-socket" interacting residues by an affinity tag.

Gretes, M.C.Karplus, P.A.

(2013) Protein Sci 22: 1445-1452

  • DOI: 10.1002/pro.2328
  • Primary Citation of Related Structures:  
    4L0U, 4L0W

  • PubMed Abstract: 
  • Peroxiredoxins (Prxs) are ubiquitous and efficient antioxidant enzymes crucial for redox homeostasis in most organisms, and are of special importance for disease-causing parasites that must protect themselves against the oxidative weapons of the human immune system ...

    Peroxiredoxins (Prxs) are ubiquitous and efficient antioxidant enzymes crucial for redox homeostasis in most organisms, and are of special importance for disease-causing parasites that must protect themselves against the oxidative weapons of the human immune system. Here, we describe reanalyses of crystal structures of two Prxs from malaria parasites. In addition to producing improved structures, we provide normalizing explanations for features that had been noted as unusual in the original report of these structures (Qiu et al., BMC Struct Biol 2012;12:2). Most importantly, we provide evidence that the unusual octameric assembly seen for Plasmodium yoelii Prx1a is not physiologically relevant, but arises because the structure is not of authentic P. yoelii Prx1a, but a variant we designate PyPrx1a(N*) that has seven native N-terminal residues replaced by an affinity tag. This N-terminal modification disrupts a previously unrecognized, hydrophobic "ball-and-socket" interaction conserved at the B-type dimer interface of Prx1 subfamily enzymes, and is accommodated by a fascinating two-residue "β-slip" type register shift in the β-strand association at a dimer interface. The resulting change in the geometry of the dimer provides a simple explanation for octamer formation. This study illustrates how substantive impacts can occur in protein variants in which native residues have been altered.


    Related Citations: 
    • Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
      Vedadi, M., Lew, J., Artz, J., Amani, M., Zhao, Y., Dong, A., Wasney, G.A., Gao, M., Hills, T., Brokx, S., Qiu, W., Sharma, S., Diassiti, A., Alam, Z., Melone, M., Mulichak, A., Wernimont, A., Bray, J., Loppnau, P., Plotnikova, O., Newberry, K., Sundararajan, E., Houston, S., Walker, J., Tempel, W., Bochkarev, A., Kozieradzki, I., Edwards, A., Arrowsmith, C., Roos, D., Kain, K., Hui, R.
      (2007) Mol Biochem Parasitol 151: 100

    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, Oregon, 97239; Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon, 97331.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thioredoxin peroxidase 1A208Plasmodium yoelii yoeliiMutation(s): 0 
Gene Names: PY00414
EC: 1.11.1.15
UniProt
Find proteins for Q7RSE5 (Plasmodium yoelii yoelii)
Explore Q7RSE5 
Go to UniProtKB:  Q7RSE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7RSE5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.076α = 90
b = 105.076β = 90
c = 41.833γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
HKL-2000data scaling
MOLREPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection
  • Version 1.2: 2018-03-21
    Changes: Source and taxonomy